Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,455,692 Δ1 bp 100% coding (1210/1260 nt) lyrA → Lysostaphin resistance protein A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,455,6920G.89.4% 181.9 / 7.6 47coding (1210/1260 nt)lyrALysostaphin resistance protein A
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base . (22/20);  minor base C (1/2);  total (24/23)
Fisher's exact test for biased strand distribution p-value = 6.08e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GCAGAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTA  >  USA300TCH1516_ALE/2455560‑2455826
                                                                                                                                    |                                                                                                                                      
gcagAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAaaaaaatta                                                                                                                                >  2:464204/1‑138 (MQ=255)
gcagAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAaaaaaatta                                                                                                                                >  2:114272/1‑138 (MQ=255)
 aataaTAAGTTAAACAAGAATCACAAAAAGACGATTTAACAAACGATTCAAATAAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAaaaaaattat                                                                                                                               <  2:367467/138‑5 (MQ=255)
     aTCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGaa                                                                                                                          >  1:376853/1‑141 (MQ=255)
      tCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAAGAAAGAGGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGaaa                                                                                                                         >  1:367206/1‑141 (MQ=255)
            aaaCAAGCACACCAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTg                                                                                                                   <  2:223307/141‑1 (MQ=255)
             atcAATCACCACAAAGGGACGACTCAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGATAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTga                                                                                                                  <  2:501905/139‑1 (MQ=255)
                  acaccacAAAGTGACGATTTAACAAACAATTCAAAGGAAGAGTAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCACAAAAA‑TTATCGAAAAAACTGAAGAAc                                                                                                             <  2:431757/140‑1 (MQ=255)
                   caccacAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCAGTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACa                                                                                                            <  2:220128/141‑1 (MQ=255)
                    accacAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACaa                                                                                                           >  2:526738/1‑141 (MQ=255)
                      cacaAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGTGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATc                                                                                                         >  2:123282/1‑141 (MQ=255)
                        caAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCtt                                                                                                       <  1:364869/141‑1 (MQ=255)
                          aaGTGACGATTTAACAAACGACTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCa                                                                                                     <  1:375770/141‑1 (MQ=255)
                           aGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAg                                                                                                    <  1:162111/141‑1 (MQ=255)
                             tGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAAAAATCTTCAGAt                                                                                                  >  2:374004/1‑141 (MQ=255)
                                agATTTAAAAAACGATACAAATGAAGAGGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATaaa                                                                                               <  2:497940/140‑1 (MQ=255)
                                           aCGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAataata                                                                                    <  1:279853/141‑1 (MQ=255)
                                              aTTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATACAAACAAATAATAACa                                                                                 <  1:516731/141‑1 (MQ=255)
                                                    aTGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAgcgc                                                                           >  2:29373/1‑141 (MQ=255)
                                                                  gtgccaTCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACctct                                                             <  1:238540/136‑1 (MQ=255)
                                                                  gagCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACATACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTAGCTAGTACctct                                                             <  1:490769/141‑1 (MQ=255)
                                                                  gagCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACctct                                                             <  1:342912/141‑1 (MQ=255)
                                                                      aaTCATTACAAGAACCTTCCACATATAAAGAAGACCTACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTccccattgac                                                         <  2:6847/141‑8 (MQ=255)
                                                                       aTCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaaa                                                        >  1:207090/1‑141 (MQ=255)
                                                                           ttAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgat                                                    >  1:546391/1‑141 (MQ=255)
                                                                             gaaaGAACCTGCGACCTATAAAGAAGACAGACGTTCATCAGTTGTAAGTGATGC‑CAAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATGATAACAAAGCGCGTGCTAGTACCTCTTAAAAAgatgt                                                  >  2:83781/2‑140 (MQ=255)
                                                                             aaaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatga                                                  >  1:359068/1‑141 (MQ=255)
                                                                              aaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCACATAAAAAgatgat                                                 >  2:399363/1‑141 (MQ=255)
                                                                                     cTGCGGCTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCa                                          <  2:515039/141‑1 (MQ=255)
                                                                                     cTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTAGCTAGTACCTCTTAAAAAGATGATGCTAGCa                                          >  2:281293/1‑141 (MQ=255)
                                                                                      tGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAGACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCaa                                         <  1:303648/141‑1 (MQ=255)
                                                                                      tGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCaa                                         >  2:199510/1‑141 (MQ=255)
                                                                                      tGCGACTTATAAAGAAGACAGACGTTCATCAGTTGGAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCaa                                         <  1:204374/141‑1 (MQ=255)
                                                                                       gCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAg                                        >  2:578511/1‑141 (MQ=255)
                                                                                       gCGAATTAAAAACAAGACAGACTTTCATCAGTTGAAATAGAAGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATCACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAg                                        <  2:372206/141‑1 (MQ=255)
                                                                                       ctcaCTTACACATAATACAGACGTTCATCAGTTGTAATTAATACA‑AAAAAAATATCGAAAAATCTGAAGAACAATCTTCAGATAAAAACAAATAATAACAATGCGCTTGCTAGTACCTCTTTAAAAGATGATGCTAGCAAg                                        <  2:419874/138‑1 (MQ=255)
                                                                                          aCTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcgc                                     >  2:409734/1‑141 (MQ=255)
                                                                                           cTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCt                                    <  1:580420/141‑1 (MQ=255)
                                                                                              ataAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAGAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCtttt                                 >  1:464258/1‑141 (MQ=255)
                                                                                               taAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTAGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTc                                >  2:35522/1‑141 (MQ=255)
                                                                                                aaaGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCCAGCGCTTTTct                               >  2:94919/1‑141 (MQ=255)
                                                                                                aaaGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTct                               >  2:555634/1‑141 (MQ=255)
                                                                                                       acagacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCCAGCGCTTTTctatactaa                        >  1:272090/1‑140 (MQ=255)
                                                                                                       acagacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctatactat                        >  2:5052/1‑141 (MQ=255)
                                                                                                          gacTTTCATCAGTTGTAATTGATGC‑CAAAAAATGATCGACAAAACTGAAGAACAATCTTCAGATAAAAATAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACtatata                     <  2:316453/141‑1 (MQ=255)
                                                                                                          gacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACtatata                     <  1:353089/141‑1 (MQ=255)
                                                                                                               tcatcaGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGGTGATGCTAGCAAGGGGTTTTCTATAGTATATattgtt                >  1:174356/1‑141 (MQ=255)
                                                                                                                 atcaGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTAtttt              >  1:101264/1‑141 (MQ=255)
                                                                                                                    aGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTTCCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCt           <  2:7797/141‑1 (MQ=255)
                                                                                                                             tGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAGGCGCTGGCTAGTACCTCTTCAAAAGAAGATGCTAGCAACCGCTTTTCTATCCTATATATTATTTTTCTAAAATTTTa  >  2:107998/1‑141 (MQ=255)
                                                                                                                                    |                                                                                                                                      
GCAGAATCAGTTAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTA  >  USA300TCH1516_ALE/2455560‑2455826

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑